The ending is but the set-up to a spinoff of the series, more war orientated and with less high-school faggotry. And it goes like this:
Britannia conquered the world thanks to their superior weapons and tactics, but this was all thanks to the helping hand of an obscure Lemuria like nation (make it Atlantis instead of Lemuria if you wish so, they're the same) that has been hidden from the rest of the world since the begging of time, this hidden nation finally reveals itself, due that the shield protecting them finally faded as V.V. killed the last member of the cult that made that shield.
The nation goes into a full huge scale war against Brittannia at the final chapters and this gives Lelouch the opportunity to finally accomplish his goal, and so another battle develops in the capital of Britannia, where the Black Knights, along with help recruited from the hidden nation, fight the Britannian royal army. After a huge climatic battle spanning 4 or 5 episodes of pure badassery, Lelouch enters the palace, only to find that the Emperor is gone, and only V.V. stands in the throne.
With a smug smirk, V.V. says: "I have killed the gods" and all of a sudden, Lelouch starts to feel weak and faints.
The battle rages on as Lelouch's closest circle of pawns escape from the scene carrying their leader, it is shown that the assault has failed in numerous stages, leaving the Black Knights in a full retreat. Lelouch enters a comatose state afterwards... everyone is puzzled with what happened.
And then, we move on to the next thingy...